An Electrospray-Tandem-Time-of-Flight Mass Spectrometer (ESPI-TTOF-MS) has been designed and built for the purpose of obtaining both molecular weight and structural information of biological molecules. The objective of this proposal is to address the issue of data capture and treatment from such an instrument. As an alternative to time averaging, it is proposed that a covariance correlation algorithm be applied to capture, store and analyze each and every mass scan for shot-to-shot variations in the intensity of each observed mass peak. In this manner, non-random variations could be quantified and returned to the user and analyses as to which masses are parents, which are daughters, and which parents are related. The aim of this research is to simplify the analysis of multi-generation mass spectra through the application of well established multivariate analytical techniques. Standard time-of-flight mass spectra using an electrospray ionization source will be used to generate data streams. Using a high speed registration system, studies will determine the necessary data transfer rates, storage capacities and computational speeds necessary for covariance correlation to be both scientifically valuable and financially feasible. Such a system would put structural identification and analysis within reach of even non-MS trained technical users.